In front of the Abandoned train in Arizona, the Professor will tell you about his plans for world domination, and says he will revive the dead into his army. Before he runs inside the train, he will say, "Go on! Die and join my army!". He will then send his Mechanical Nightwalkers to fight you in three waves, before he fights you using his Flamethrower. He will not die in the end; instead he will just run away, saying that he will seek revenge.

It's best to fight him from some distance as his Flamethrower has limited range, though its flames will still reach half of the given mission area. One way to evade him is circling him. The flames will reach the space in front of you, but won't hit you.